Structure-guided bifunctional molecules hit a DEUBAD-lacking hRpn13 species upregulated in multiple myeloma

Xiuxiu Lu; Venkata R Sabbasani; Vasty Osei-Amponsa; Christine N Evans; Julianna C King; Sergey G Tarasov; Marzena Dyba; Sudipto Das; King C Chan; Charles D Schwieters; Sulbha Choudhari; Caroline Fromont; Yongmei Zhao; Bao Tran; Xiang Chen; Hiroshi Matsuo; Thorkell Andresson; Raj Chari; Rolf E Swenson; Nadya I Tarasova; Kylie J Walters

doi:10.1038/s41467-021-27570-4

Structure-guided bifunctional molecules hit a DEUBAD-lacking hRpn13 species upregulated in multiple myeloma

Nat Commun. 2021 Dec 16;12(1):7318. doi: 10.1038/s41467-021-27570-4.

Authors

Xiuxiu Lu¹, Venkata R Sabbasani², Vasty Osei-Amponsa¹, Christine N Evans³, Julianna C King³, Sergey G Tarasov⁴, Marzena Dyba⁴, Sudipto Das⁵, King C Chan⁵, Charles D Schwieters⁶, Sulbha Choudhari⁷, Caroline Fromont⁸, Yongmei Zhao⁷, Bao Tran⁸, Xiang Chen¹, Hiroshi Matsuo⁹, Thorkell Andresson⁵, Raj Chari³, Rolf E Swenson², Nadya I Tarasova¹⁰, Kylie J Walters¹¹

Affiliations

¹ Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
² Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
³ Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
⁴ Biophysics Resource, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
⁵ Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, 21702, USA.
⁶ Computational Biomolecular Magnetic Resonance Core, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-5620, USA.
⁷ Sequencing Facility Bioinformatics Group, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA.
⁸ Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA.
⁹ Basic Science Program, Center for Structural Biology, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
¹⁰ Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
¹¹ Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA. [email protected].

Abstract

Proteasome substrate receptor hRpn13 is a promising anti-cancer target. By integrated in silico and biophysical screening, we identified a chemical scaffold that binds hRpn13 with non-covalent interactions that mimic the proteasome and a weak electrophile for Michael addition. hRpn13 Pru domain binds proteasomes and ubiquitin whereas its DEUBAD domain binds deubiquitinating enzyme UCHL5. NMR revealed lead compound XL5 to interdigitate into a hydrophobic pocket created by lateral movement of a Pru β-hairpin with an exposed end for Proteolysis Targeting Chimeras (PROTACs). Implementing XL5-PROTACs as chemical probes identified a DEUBAD-lacking hRpn13 species (hRpn13^Pru) present naturally with cell type-dependent abundance. XL5-PROTACs preferentially target hRpn13^Pru, causing its ubiquitination. Gene-editing and rescue experiments established hRpn13 requirement for XL5-PROTAC-triggered apoptosis. These data establish hRpn13 as an anti-cancer target for multiple myeloma and introduce an hRpn13-targeting scaffold that can be optimized for preclinical trials against hRpn13^Pru-producing cancer types.

Publication types

Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural

MeSH terms

Apoptosis
Cell Line, Tumor
Gene Expression Regulation, Neoplastic
Humans
Intracellular Signaling Peptides and Proteins / chemistry*
Intracellular Signaling Peptides and Proteins / genetics
Intracellular Signaling Peptides and Proteins / metabolism*
Multiple Myeloma / genetics
Multiple Myeloma / metabolism*
Proteasome Endopeptidase Complex / metabolism
Transcription Factors / metabolism
Transcriptional Activation
Ubiquitin / metabolism
Ubiquitination*

Substances

ADRM1 protein, human
Intracellular Signaling Peptides and Proteins
Transcription Factors
Ubiquitin
Proteasome Endopeptidase Complex

Abstract

Publication types

MeSH terms

Substances

Grants and funding